Submission outputs API endpoint fails for 'orchestration' WDLs
If you have a WDL that imports other WDLs to run, but the top level WDL has no tasks/calls of its own, then the API endpoint for getting submission outputs fails. Example:...
View ArticleUploading files from GP@Broad
We have all of our sequencing files for WGS and RNA-seq stored in the genomics platform of the Broad and we only have paths to these files. I am wondering how to upload these files to the Firecloud?
View ArticleMetadata formatting
This discussion was created from comments split from: Getting error when uploading the genomic data model.
View ArticleQuota on GPUs per billing account leads to job failures rather than queueing
Hi Firecloud team, I am running a gpu task on ~1300 samples and have started running into this error: The job was stopped before the command finished. PAPI error code 2. failed to insert instance:...
View Articleproblem with accessing files in a Google bucket
Dear Firecould team. I get the following access error message when I try to access a workspace I used to have access to: The Google bucket associated with this workspace is currently unavailable. This...
View ArticleRAWLs errors in submission
I submitted a batch job and two of the workflows immediately failed with two separate rawls errors: ErrorReport(rawls,http error calling uri...
View ArticleTest for new ticketing system
Hello FireCloud users, Please ignore this thread. It is temporarily being used to test our new ticketing system to allow us to better answer your questions. Have a great day!
View Article403 Error from FireCloud
Single Cell Portal received 403 errors from FireCloud: E, 2018-08-17T10:45:10.218293 #30059 ERROR – : 1058e905-3df6-4663-b1f0-1bd8966ffc31 2018-08-17 10:45:10 -0400: 403 Forbidden encountered when...
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Scatter jobs don't run
I'm not sure if this is a scatter problem or just a general FireCloud issue. Some of my jobs in the scatter job fail almost immediately with the following error message: message: Task...
View ArticleMethod added to repository via API not showing up in UI
I'm working on some integration for a new application that will add methods to the Methods Repo (via the API) on behalf of users. Everything works properly, but I'm noticing something strange with the...
View ArticleDocker file mapping error?
Hi, I'm using a Wdl that I've used for cellranger back in June successfully, but now I am getting a strange docker file mapping error. In the logs file, it used to say "Docker file...
View ArticleIs there runtime parameter for number of vCPU?
I see runtime parameters for memory and defaultDisks, but can you set number of CPUs?
View ArticleError-cannot start job in WorkflowExecutionFailingState state with restart
I'm getting the error " Cannot start job in WorkflowExecutionFailingState state with restart". What does this mean? Thanks.
View Articlemounting data somehow other than by copying?
In one of my pipelines, the first step is downloading a 30G tar.gz file from a bucket followed by unpacking it. This takes a considerable amount of time. Is there a way to mount a read-only filesystem...
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joint-discovery-gatk4 failures
Hi I've been trying to run joint-discovery-gatk4 (copied from workspace help-gatk/Germline-SNPs-Indels-GATK4-b37 ) on a sample set of 254 WGS bams and have been experiencing many failures with subtle...
View Articlefeature request: make wdl editor window expandable
In the firecloud wdl editor, the editor window doesn't appear to be expandable, but the comment window below is. It would be helpful for the wdl editor to be expandable to increase the viewing /...
View ArticleFireCloud Error: processing-for-variant-discovery-gatk4
I tried to run the method "processing-for-variant-discovery-gatk4" cloned from the featured workspace "Germline-SNPs-Indels-GATK4-b37" on some of my samples. I only made 2 changes to the configuration:...
View Articlepreempted job w/ no caching set to failed state
Hi, I received the following for a job: 2018-08-24 15:28:18,726 INFO - PipelinesApiAsyncBackendJobExecutionActor [UUID(43bd5380)ctat_fusion_wf.CTAT_FUSION_TASK_FQPAIRTARGZ:NA:1]: Status change from...
View Articlejob supposedly running for 9 hrs, but no output... and no evidence of execution
Hi, I've got a bunch of jobs that have been running for ~9 hours (and they're expensive jobs, using moderate-mem machines), and I can't seem to find evidence of them doing anything. The buckets just...
View ArticlePublic method fails when submitted by non-Broad email from Broad-owned project
I am doing some testing on the Unity service, and I ran into an issue with submissions that I have not been able to deduce what the problem is. Background: I'm adding methods to the method repo as...
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